I initialized my "int SPCounter= 25;" and on the vero board proto UNO it displays that SPcounter as 25. Which is correct,exactly what I wanted..but on my prototype, the SPCounter is initialized at 256. Which is not correct..
Are we supposed to assume that your prototype uses the same ATMega328 chip that the UNO uses?
I have used command prompt avrdude to erase the flash and eeprom, but everytime my SPcounter starts at 256.
I'm sorry, but this statement is nonsense. You do NOT display the value in SPCounter until after you have trashed the initial value with what you read from EEPROM and possibly incremented.
255, the default value for uninitialized EEPROM cells, + 1 IS 256.
No amount of diddling with erasing the flash or EEPROM is going to put anything BUT 255 in the cells. YOU must write some other value there if you expect to read some other value.